Glossina palpalis gambiensis and G. tachinoides are the main vectors of human and animal trypanosomoses in West Africa. In some parts of their distribution area, they co-exist in sympatry, but little is known about their interactions. This study aimed to explore their respective flight height and daily activity when co-existing or alone. Attractive targets were used, made of a black/blue/black cloth covered with adhesive film, so that all tsetse that landed were caught. The study was conducted in two areas in South Burkina Faso: Kartasso, upstream the Mouhoun river, where G. p. gambiensis is the only tsetse occurring; and Folonzo, on the Comoé river, where both species occur. Out of more than 3,800 tsetses caught in total, in Folonzo, G. tachinoides occurred at higher densities than G. p. gambiensis (84 vs 16% of the total densities). The mean height of capture was 55 cm for G. tachinoides, and 65 cm for G. p. gambiensis. As a comparison, in Kartasso where G. p. gambiensis is alone, the mean height of capture was 46 cm, these differences being statistically significant. In average, females were caught higher in altitude than males, and the two species showed a similar activity profile in the day. These results are discussed in the light of differences in the nature of the forest gallery, or possible interspecies competition behaviour in relation with their limited energy metabolism and flight capacities, or also with species differences in landing behavior, linked to host feeding detection. These observations have consequences on control tools releasing attractive odours, which may have contrasted efficacy depending of the flight height of the species.